Mystery Boxes are boxes Mario can access in Super Mario 3D Land and Super Mario 3D World. In the former game, they are found in most Worlds, with their primary task being to defeat all the enemies in the box within ten seconds. Enemies can range from Goombas to Boom Booms. When Mario completes the task, Coins and a Star Medal appear. Other items, such as 1-Up Mushrooms, Super Leaves and Fire Flowers are also found within Mystery Boxes. However, if Mario loses a life in a Mystery Box, he will be forced to quit the level. Whenever the player encounters a Mystery Box on the world map, he or she is required to enter it before moving on. The Mystery Box theme is a remix of the Teleporter theme from Super Mario Galaxy 2.

A golden Mystery Box. Note that there are two Star Medals and even a P-Wing.

Mystery Boxes can also be golden on the inside, while still appearing purple on the outside. All of the golden-sided Mystery Boxes contain two Star Medals, and at least three 1-Up Mushrooms, with some containing as many as eight. No golden-sided Mystery Boxes contain enemies, and as such, Star Medals appear immediately upon entering a box. They can contain many different things, such as Poison Mushrooms, Toads, or even P-Wings. These Mystery Boxes have a cover of the main theme from Super Mario Bros. as the background music.

There are a total of 20 unique normal Mystery Box contents and 15 unique golden-sided Mystery Boxes contents. Golden-sided Mystery Boxes are less likely to appear than normal ones. Each normal Mystery Box can be found in two different Worlds, while each golden-sided one can only be found in a single World.

After completing a Mystery Box, it turns gray on the Overworld Map, "falls asleep", and becomes inaccessible. It may be accessed again 20 hours later. The contents of each Mystery Box changes each time it is re-entered.

Mystery Boxes can also be accessed via StreetPass (a wireless feature that automatically exchanges infomation with other 3DS holders while the system is in sleep mode). The only difference in a StreetPass Mystery Box is that it is guaranteed to have a Star Medal or two, unless of course all Star Medals have been collected.

Mystery Boxes also can appear in some levels of Super Mario 3D Land, which the goal is to collect as many coins from the blocks within the time limit.

Mystery Boxes in Super Mario 3D World can only be found in levels. Each of them has a Green Star which must be collected within the time limit. If Mario fails, he is sent back to the proper level. The Green Stars must be collected in different ways, like defeating every enemy present, navigating through a small obstacle course, or using given items or forms to reach it. Certain worlds also feature special courses called Mystery Houses, which consist of clearing a number of Mystery Box courses in quick succession. In one area of the Shifty Boo Mansion level, the Boo painting is the real Mystery Box and if the players picks the Mystery Box, it becomes a decoy and a Boo will appear to distract Mario.